Animation after applied modifier
You can animate [render visibility] with Keyframes. The graph window can show render visibility of multiple objects at once. This may address part of your issue. Other people can address other concerns or you can submit a different question.
Of course in Blender there are always 33 ways to do something.  You can use layers as well or simply move an object out of view of the camera.  You can also consider other visual cues such as viewing only edges .. and or keyframed scale factors.

The yellow arrows shows the effects of putting a keyframe on render visibility of an object. Please Click on the image to see a larger version.  By having two or more objects you can instruct Blender to render one of them and to not render the other ones, saving compute time.  Please do not confuse this with 3D View Visibility.  This is not a tutorial.